U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125387279 Sharpr-MPRA regulatory region 13247 [ Homo sapiens (human) ]

Gene ID: 125387279, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125387279
Gene description
Sharpr-MPRA regulatory region 13247
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, May 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC125387279 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (46207950..46208244)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47944016..47944310)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17960 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44731180-44731415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17962 Neighboring gene CRISPRi-FlowFISH-validated CD40 regulatory element GRCh37_chr20:44746135-44748232 Neighboring gene ribosomal protein L13 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17967 Neighboring gene CD40 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44781551-44782092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12973 Neighboring gene uncharacterized LOC124904916 Neighboring gene cadherin 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44844486-44845022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44845561-44846096 Neighboring gene MPRA-validated peak4226 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44886736-44887236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44928578-44929078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44929079-44929579 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44932028-44932246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44941853-44942801 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44952422-44952611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44966161-44966662 Neighboring gene Sharpr-MPRA regulatory region 3506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44979919-44980510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44980511-44981101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44985189-44985688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12974 Neighboring gene uncharacterized LOC124904917 Neighboring gene solute carrier family 35 member C2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17971 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:45022873-45023372 Neighboring gene engulfment and cell motility 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_080955.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    46207950..46208244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    47944016..47944310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases